Month: October 2015

Today in EvoLiteracy News: A recent study about the authenticity of the Shroud of Turin caught my attention for two reasons. First, it was published in Scientific Reports, a science-media outlet sponsored by Nature. Second, five authors believed to have tested two “hypotheses” when, in reality, they reconfirmed –indirectly– support for an old thesis (i.e. the Medieval origin of the shroud, 800 years ago) and speculated over a historicity-based idea (i.e. that the shroud originated in Jerusalem, 2000 years ago, and it was later transported to Turin). The study is an exemplar of conceptual error, and it can be used in scientific-methodology courses to educate our students on how to avoid making similar mistakes. – Guillermo Paz-y-Miño-C

Shroud of Turin, Poor Science, and the Persistence of a Myth

I will dedicate some length to examine this study (Uncovering the Sources of DNA Found on the Turin Shroud), which falls apart by itself when attempting to combine modern DNA analysis with a silly, pseudoscience project: to find scientific evidence to justify believing in a myth. The concerning part is that five authors, Barcaccia et al., were fortunate to publish the research (October 5, 2015) in Scientific Reports, a fairly known science-communication venue.

Negative of the Shroud of Turin printed as positive 1898

The team examined “two” hypotheses, one scientific, the other a historicity supposition. The scientific thesis –for which Carbon dating has provided unequivocal evidence since 1988/9— is that the Shroud of Turin is a fake, a fabrication of Jesus’ body’s imprint on ordinary linen traceable to the 13th and 14th centuries, specifically to 1260-1390 (C-dating is quite accurate). The historical supposition, in contrast, suggests that the shroud must have come from the years 30 or 33, of modern times, which makes it a 2000-year-old relict. The latter has no scientific sustain. But the authors build up –in a technical report format– the argument that their molecular analyses bring support to “both” hypotheses (Medieval origin and Jesus’ timeline). This is not the case. In fact, it is impossible to merge both proposals because the shroud is 800 years old, while the Jesus-person tale –if real– is three times older. Therefore, there is an irreconcilable mismatch in time between the two views.

Readers can judge the study for themselves (at this link), but I prefer to summarize the reality of its findings –while avoiding the authors’ convoluted logic– as follows:

First, Barcaccia et al. admit that the Carbon-dating piece of evidence –a crucial element in this case– demonstrates that the Shroud of Turin originates in Medieval times (statistical confidence 95 percent). That is, we are pretty sure that the linen does not come from 2000 years ago. The shroud is one third the age it is supposed to be under the historicity hypothesis. Therefore, everything else upon which the authors speculate in the study is irrelevant. The Barcaccia et al. conjectures, no matter how the investigators spin them, are inconsistent with the Carbon-dating clock: 800 years old.

Second, the shroud is contaminated with plant material (particularly pollen, which can be detected via chloroplast DNA analysis) belonging to plant species from, almost, all over the world (see figure below). Because the shroud’s linen is 800 years old, the contamination must have occurred during recent times.

Plant DNA species found on the Shroud of Turin. Schematic overview of the centers of origin of plant taxa identified in samples of the shroud. Image source Barcaccia et al. 2015.

Third, the linen of the shroud is also heavily contaminated with human DNA (detected via mitochondrial DNA profiling; see figure below), which belongs to multiple individuals, from multiple ethnic backgrounds and, therefore, from multiple geographic locations (Europe, West Asia, Northeastern Africa, Arabia, Middle-East, all the way down to India –not from the Americas). Again, because the shroud is 800 years old, human contact with it must have occurred during recent times.

Human mtDNA haplogroups found on the Shroud of Turin. Schematic overview of the current geographical distribution of human mtDNA haplogroups and sub-haplogroups identified in samples of the shroud. Image source Barcaccia et al. 2015 (click on it to enlarge).

Fourth, and this is not a trivial finding, although the authors report it as extraneous, the shroud is also contaminated with DNA from the bird Southern Grey Shrike (Lanius meridionalis), distributed in Southwest Europe, Northern Africa, the Near East, and Southwest Asia. And also with genetic traces of a marine Nemertine worm (Cerebratulus longiceps), from the Northern Pacific Ocean (species description from Alaskan samples, 1901). Once more, as it becomes crucial to remind the readers, because the shroud is 800 years old, bird- or marine worm-DNA must have contaminated the fabric during the past eight centuries.

Fifth, despite these findings, the authors bend over backwards, put aside the age of the shroud and free fall into speculating that if we –somehow– eliminate the noise of the overwhelming DNA contamination, we can “parallel” the genetic patterns of human DNA contamination with the historical path taken by the shroud’s carriers, allegedly from Jerusalem to Turin. A sort of “spatial” retracing of the shroud’s migration. That is, an attempt to find in the genetic markers –which in reality only inform us about the diverse geographic sources of the DNA contaminants– the evidence in support for the historicity hypothesis: Hhthat the linen has traveled from Jerusalem to Turin, and via human hand-to-hand (with occasional bird or marine worm intervention) along an envisioned route. And this way of reasoning –by Barcaccia et al.– is so troubling, because it is a blunt Type One Error, a conceptual violation of scientific scrutiny. It picks and chooses what type of contaminant DNA is more informative than other (when all of them are, in principle, contaminants of a cloth one-third the age it is supposed to be), in order to fit the authors’ wish to force support for the historicity hypothesis. And this is done in plain sight of an 800-year young cloth or, in fact, a fake 2000-year-old-wanna-be relic.

“…To be authentic, the Shroud of Turin must be 2000 years old. It is not. Carbon dating places it only eight centuries ago, in Europe. And there is no evidence to link the shroud to Jerusalem, and to the years 30 or 33.”

Sixth, what Barcaccia et al. seem to have found, after cleaning some of the noise in the multiple genetic contaminations (i.e. by discarding some contaminants and keeping “informative” DNA sequences) is an artifact, a byproduct effect of the spatial source of the contamination, that gives the impression of a geographic pattern of migration of the shroud (from Sacred Land to Turin). In reality, it is a pattern of the source of the contamination (not a reflection of the origin of the shroud), consistent with the history of human-worshipers’ approaches to the linen, to touch it. This actually explains the apparent absence of human DNA contaminants from the Americas in contrast to the more-likely-contaminants to be found: the people living nearby the shroud, from the years 1200-1300s onwards. And this is a more parsimonious explanation to the Barcaccia et al.‘s speculations. The authors could have just rationalized over a 2×2 table (see figure below) when designing the tests for: Medieval-origin hypothesis (spatial and temporal evidence) and historicity hypothesis (spatial and temporal evidence). In other words: Medieval-origin hypothesis (Europe and 800 years) and historicity hypothesis (Jerusalem and 2000 years). It becomes obvious that the authors cannot combine, in any manner, one hypothesis with the other because the proposals do not match in time (the time dimension). Therefore, any spatial speculation of consistency, as Barcaccia et al. propose, is senseless. More so when the spatial argument for “possible parallelisms” between hypotheses relies on the capricious use of DNA-contaminants and the exclusion of the timeframe disparity (800 vs. 2000 years). Poor science, indeed.

To be authentic, the Shroud of Turin must be 2000 years old. It is not. Carbon dating places it only eight centuries ago, in Europe. And there is no evidence to link the shroud to Jerusalem, and to the years 30 or 33. A: spatial evidence for the Medieval origin hypothesis vs. the Historicity hypothesis; European art techniques used to fake the shroud have been confirmed vs. the genetic contaminants used to speculate that the shroud may come from the Sacred Land. B: Temporal vs. spatial evidence; radio Carbon-dating places the shroud 800 years ago, which is inconsistent with the hypothetical Jerusalem origin. C: Temporal vs. spatial evidence; the hypothetical 2000-year-old age of the shroud is inconsistent with the Medieval European art techniques used to fake it 800 years ago. D: Temporal vs. temporal evidence; the 2000 years of age required for the hypothetical Jerusalem origin of the shroud is inconsistent with the actual 800 years of age determined by Carbon-dating. – GPC

CONCLUSION: Barcaccia et al. study is another, among many, in-text acknowledgments that the shroud of Turin is a Medieval fake, only 800 years young (C-dating) and not a 2000-year-old relic (as demanded it to be in any test of the historicity hypothesis). Reality occurs in a space-time context, yet the authors chose to put time aside to facilitate survival of the historicity tale. The shroud is heavily contaminated with plant, human, bird and marine worm DNA, a phenomenon enhanced exclusively during the past eight centuries, during which the linen has had increasing exposure to people –and their debris, including critters’ goo– from Europe and nearby locations (not to mention the rest of the world). The genetic spatio-temporal mapping presented by Barcaccia et al. reflects a pattern of contamination by humans of multiple ethnicities, consistent with convergent traveling, from diverse locations, in the direction to the object, the shroud, possibly to worship it. If anything, this paper documents the spatial distribution of human contamination of the linen from likely-geographic locations. It fails to provide any evidence in support of the historicity hypothesis (due to the time dimension incongruity), and it actually strengthens the notion that the shroud of Turin is a Medieval fake. The study by Barcaccia et al. is exemplar of how far poor judgment can go, and how belief in supernatural causation disrupts, distorts, delays or stops (the 3Ds + S cognitive effects of illusory thinking) the acceptance of scientific evidence before the very eyes of the investigators, and with their own data. – GPC

Negatives (left and right images) of the Shroud of Turin. The cloth is about 14 x 4 ft.

VIDEO: Click on image below to be redirected to NatGeo video Remaking The Shroud, in which techniques for faking it are discussed, and some modern-technology tests shown, including UV light and 3-D imaging.

Today in EvoLiteracy News: Louder Vocalizations in Howler Monkeys Correlate with Small Testicles. The significance of this study is the simultaneous test of three hypotheses (vocal competition, environmental adaptation and size exaggeration) and the elegant documentation of an “evolutionary trade-off” in which vocalizations (rather than the usual morphological traits) are involved. Enjoy! – GPC

Darwin wrote: “…The vocal organs of the American Mycetes caraya [Alouatta caraya] are one-third larger in the male than in the female, and are wonderfully powerful. These monkeys in warm weather make the forests resound at morning and evening with their overwhelming voices. The males being the dreadful concert, and often continue it during many hours, the females sometimes joining in with their less powerful voices… Whether most of the foregoing monkeys have acquired their powerful voices in order to beat their rivals and charm the females, or whether the vocal organs have been strengthened and enlarged through the inherited effects of long-continued use without any particular good being thus gained, I will not pretend to say; but the former view, at least in the case of [another primate] the Hylobates agilis [the gibbon*], seems the most probable…” (The Descent of Man and Selection In Relation to Sex, 1871).

[*Darwin highlights that the gibbon (H. agilis) “…is remarkable from having the power of giving a complete and correct octave of musical notes, which we may reasonably suspect serves as a sexual charm…]

A new study published in Current Biology explains that hyoid bones (crucial for roars in Alouatta) are highly sexually dimorphic, vary among species and with greater sexual dimorphism in species with larger hyoids. The study examines a phenomenon called “evolutionary trade-off;” a situation in which the enhanced expression of one trait (hyoid bone) is directly associated with the diminished expression of another (size of testicles). The assumption is that both traits are costly for an organism to express and, therefore, the trade-off resides in allocating resources to only one of them, for optimization.

Here is the story: All species of howler monkeys have a modified larynx with an enlarged hyoid bone, which works as a resonance chamber. Howls are energetically expensive to produce (link to video below). Now, what is the connection between the monkeys’ vocalizations and the size of their testicles? The study, authored by Dunn et al. (nine co-authors), explores three hypotheses: vocal competition (i.e. acoustic signals announce presence during defense of territories), environmental adaptation (i.e. hyoid bones are important for sound frequency adjustments in dense forests), and size exaggeration (i.e. voluminous hyoids work as enhancers of the acoustic impression of body size conveyed by roars).

RIGHT: Skeleton of a male Alouatta in which the hyoid bone is clearly visible –throat region. LEFT: two images of the hyoid bone showing its chamber-like structure (top) and smooth surface and elongated shape (bottom). The hyoid is very robust (made mostly of compact bone tissue).

Dunn et al. found support for the vocal competition and size exaggeration hypotheses, but not for the environmental adaptation. Here are some of the authors’ generalizations:

(1) males of various species, who live in larger groups of males, have smaller hyoid bones (panel A in figure below) and larger testicles (panel B), the latter an adaptation for sperm-sperm competition (the trade-off: because both roars and sperm production are expensive, only one trait is conspicuously expressed);

(2) males with large hyoid bones have smaller testicles (panel C in figure above; the trade-off again; these monkeys usually live in single-male-and-many-females groups);

(4) all howler monkey species produce very low-frequency vocalizations in respect to their body mass and in contrast to other mammals or corresponding body mass (see figure below; also consistent with the size exaggeration hypothesis). – GPC

VIDEO: Take a look at the energetic movement of the thorax while this howler monkey vocalizes; the entire anatomy participates in the roaring. In the rainforest, howler monkeys’ vocalizations can heard from kilometers away.

Breaking News – New Species of Galapagos Tortoise is Identified

Sorry for the introductory drama. Today, my pick for EvoLiteracy News includes a study just published -hours ago- in PLoS ONE. A characterization of a distinctive lineage of Galapagos Giant Tortoises. The study is rich in data; below I summarize its major points. Enjoy! – GPC

The two populations of Galapagos tortoises in Santa Cruz Island apparently belong to separate species. Click on image to enlarge.

First, the discussion over the “correct genus” of the Galapagos tortoises has been vivid since 1914, with three justified proposals: Testudo (14 species: 1914), Testudo elephantopus (all subspecies, 1955), Geochelone (as genus, 1957) and Chelonoidis (as sub-genus of Geochelone, 1957). The latest proposal is that all sub-species (13 or 14), or valid biological species, should be placed within Chelonoidis (2006), as legitimate taxa (the problem with Geochelone is that it seems to be polyphyletic, a fancy word to imply “artificial” rather than a natural group, as Chelonoidis).

The skull of the holotype (i.e. the representative specimen) used for description of Chelonoidis sp. nov. from Cerro Fatal, Santa Cruz. Click on image to enlarge.

Fourth, the new species is described for Santa Cruz Island. It belongs to a separate population (Chelonoidis donfaustoi sp. nov., from “Cerro Fatal,” estimated divergence 0.43 million years ago), genetically distinctive and only 20 Km distant from Chelonoidis porteri (from “Reserva,” estimated divergence 1.74 million years ago).

Fifth, the new species C. donfaustoi is genetically identifiable (via nuclear microsatellite and mitochondrial DNA), which suggests reproductive isolation.

Sixth, the new species has only 250 surviving individuals, which makes it one of the rarest, possibly one of the most endangered lineages of extant Galapagos tortoises.

CONCLUSION: The paper by Poulakakis et al. (total 12 authors), which was published today in PLoS ONE, is interesting and well documented. Keep in mind, however, that populations naturally –and not unusually– move, drift over time, colonize environments, become isolated, and gradually diversify (i.e. the foundation of species radiation). In this respect, the study adds specificity to our previous understanding of the Galapagos tortoises’ population genetics. It gives us additional hints about island connectivity during the geologic past of the archipelago; for example, if we look closely into the mtDNA (mitochondrial) haplotype phylogeny of the extant and extinct tortoises, including museum specimens (below), the newly described “species” (C. donfaustoi) branches as sister taxa of the San Cristobal Island tortoise C. chathamensis, today a separate island, but likely connected to Santa Cruz in the past. Hopefully, the study by Poulakakis et al. generates support to conservation efforts (funding) of these magnificent giant tortoises. – GPC

“…Mutations are essential to evolutionary change; they provide the genetic variability that lineages of organisms need to persist over the eons. At the same time, evolution has equipped our cells with repairing mechanisms to fix, edit DNA errors that can be detrimental…”

If completely stretched into a single, long molecular chain, the DNA of a human cell would measure about two meters. During our lifetimes, our bodies would replicate enough DNA that, theoretically, it could be extended from Earth to the Sun, and back, 250 times. Ample opportunities to accumulate 37 trillion mutations while re-copying the genetic material.

DNA-repair, image by Tom Ellenberger, Washington University in St. Louis.

What I admire most in these investigators is their obsessive pursue of knowledge during a vigorous exploration of the intimacy of our inner molecules. As Modrich puts it “curiosity-based research is so important; you never know where it is going to lead.” And it did lead them from almost extraneous observations of the harmful effects of UV-light on the DNA of bacteria to –four decades later— its applications to our current understanding of cancer, neuro-degenerative disorders and ageing. Another lesson for today’s academic administrators infatuated with worshiping the science-for-profit model.

All began in the 1920s when American geneticist Hermann Muller (Nobel Laureate in Physiology or Medicine, 1946) found that X-rays could harm bacterial cells. By the 1940s, it was known to scientists that UV-light also had mutagenic effects on most cells. Interestingly, despite radiation-induced damage in bacteria, laboratory colonies continued to persist, which led researchers to infer that these organisms had repair-mechanisms to reinstate the internal chemistry. In 1944, DNA was recognized as the material of heredity and UV-light as a deteriorating agent of its structure.

“…What I admire most in these investigators is their obsessive pursue of knowledge during a vigorous exploration of the intimacy of our inner molecules… [Their] story only grows in beauty…”

The first breakthrough in DNA-repair mechanisms was unexpected: Albert Kelner (US) discovered that, in response to UV-induced cellular damage, bacterial enzymes could reverse the process by using –surprisingly— light, and capturing its energy-particles (photons), which excite electrons in the enzymes’ functional parts, thus jump-starting their repairing engines. The process was termed photo-reactivation and the enzymes photolyases. The story only grows in beauty.

Keep in mind that DNA is built of four “bases,” called adenine A, guanine G, cytosine C and thymine T. Under ordinary circumstances, A always pairs with T, and G with C, hence forming the steps of the DNA’s double helix, which is usually depicted as a staircase. In 1974–1976, Tomas Lindahl studied a frequent mutation in which G, rather than pairing with C (as G-C), had, as partner, the base U (uracil), a constituent of other molecules in the cell. Why? C and U are very similar, but when C loses some of its parts, due to predictable chemical contingencies, it can resemble U more closely. Thus DNA would temporarily accept the pairing G-U, but the cell would fix it by enzymatically chopping off U and restoring the correct coupling G-C. And Lindahl mapped, so elegantly, this entire process, which was labeled single-base excision repair. Later, it became part of the cell’s toolbox for DNA repair mechanisms, of which numerous have been described.

Illustration: Johan Jarnestad – The Royal Swedish Academy of Sciences (click to enlarge).

In a separate study, Aziz Sancar experimentally manipulated with UV-light-induced mutations and characterized how the cell could fix errors via an alternative pathway, termed multiple-base excision repair, which included cutting off several bases, not only one, as described by Lindahl. Sancar knew that UV-light could make T behave strangely and pair with its homologue (T-T), rather than with A, as it normally does (T-A).

Let us imagine two parallel rows of DNA sequence in which the top one is G,C,T,T,C,G. Its complementary, bottom, pairing (following the rule A-T and G-C) would be C,G,A,A,G,C. However, UV-light damage can induce the Ts on the top row to pair with each other, as T-T, rather than with their corresponding As in the bottom, as T-A and T-A. Thus creating a bump loop on the top row (T-T), leaving the As in the bottom unpaired.

In 1983, Sancar plotted the entire mechanism of repair of the T-T mutation, which included multiple enzymes responsible for accurately cutting and restoring 12 bases in the top row of DNA, five prior and five post T-T. An amazing work.

Illustration: Johan Jarnestad – The Royal Swedish Academy of Sciences (click to enlarge).

By 1989, Paul Modrich had unveiled a third mechanism, which involved the fixing of DNA sequence mismatches, which randomly emerge during cell divisions. A process called DNA mismatch repair. It included even larger stretches (beyond 12 bases) of folded DNA, which specific enzymes would cut and restore to the correct sequence (watch VIDEO).

Illustration: Johan Jarnestad – The Royal Swedish Academy of Sciences (click to enlarge).

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“This is an inspiring, readable collection of essays of reflective value to everyone. Paz-y-Miño-C points to the vain attempt by many to try and accommodate scientific rationalism with supernatural beliefs. They are simply incompatible. The author has a marvelously eloquent style of writing, full of inspiring metaphors and lateral observations that reinforce connections to the foundations of scientific inquiry and to biological evolution in particular. These thoughtful essays… are inspiring… [and] help clear the fog in our communities and arm our neighbors [with arguments] against theistic anti-science, medical quackery and other irrational nonsense.” – Greg M. Stott, PhD, Geoscientist with the Ontario Geological Survey, Canada.

“Paz-y-Miño-C doesn’t ask the reader to ‘believe’ in evolution. He provides overwhelming evidence, clearly written, that shows how scientific inquiry leads to important and practical results, while superstition and faith lead nowhere. Although we may not be able to reason someone out of what they were never reasoned into, the author presents a roadmap for those whose minds are open to discover the wonders and beauty of science.” – Herb Silverman, PhD, author of Candidate Without a Prayer: An Autobiography of a Jewish Atheist in the Bible Belt.

“Too many of our colleagues work so hard to appear open minded that their brains seem to have fallen out. When they teach our students that they can pick and choose when to be logical, critical thinkers, they are modeling the type of reasoning that leads to the politics of convenience and its bridesmaids: racism, sexism, and the whole host of xenophobias. Paz-y-Miño-C is a prolific essayist, he does not pull any punches, but when he cuts to the core of an argument, he does it with the flare of a true artist.” – Stan Braude, PhD, Professor of Practice in Biology, Washington University in St. Louis, USA.

Each of three parallel workshop sessions was attended by about 20 people. I enjoyed our session (The Values of Science) very much, perhaps precisely due to the size of the meeting, the diversity of scholars participating (i.e. sociologists, chemists, anthropologists, philosophers, physicists, biologists, educators, media specialists), and the interdisciplinary format of the discussions.

The Values of Science

Anti-scientism and Its Impact on the Relationship between Science and Religion: The Role of Science in a Postmodern Society. Dr. Mohamed Almisbkawy, Department of Philosophy, British University in Egypt, Fayoum University, Cairo, Egypt. Overview: The clash between classic science and religion was due to the similarly in their internal structures. Science has overcome this nature of scientific system by shifting from scientism to anti-scientism.

Evolution Controversy: A Phenomenon Prompted by the Incompatibility between Science and Religious Beliefs. Dr. Guillermo Paz-y-Miño-C, New England Center for the Public Understanding of Science and New England Science Public, Roger Williams University, Bristol, USA. Dr. Avelina Espinosa, New England Center for the Public Understanding of Science and New England Science Public, Roger Williams University, Bristol, USA. Overview: This paper explores the evolution controversy under three predictions of the incompatibility hypothesis.

Some of the images used in our presentation at the VII International Conference on Science in Society, Chicago, October 1-2, 2015. We discussed in detail the Incompatibility Hypothesis.

Formally Trained Science Communicators: A Solution to the Unreasonable Expectations Placed on Lay People and Professional Scientists. Dr. Teresa Branch-Smith, Department of Philosophy, University of Waterloo, Waterloo, Canada. Jay Michaud, Department of Philosophy, University of Waterloo, Waterloo, Canada. Overview: We need to formally train science communicators to facilitate the transmission of knowledge from scientists to people because it requires expertise that neither group should be expected to acquire independently.

Our hostesses and organizers of the VII International Conference on Science in Society at The University Center Chicago, October 1-2, 2015.

The complete article, which includes 23-pages, 11 figures and 59 references, can be downloaded —for free— from the International Journal of Science in Society. Click on the image (left) to go to the journal website to download the PDF.